R devel - Apr 2008 - Windows problem related to using shortPathName for Sweave style file

In the process of updating R to R 2.7 alpha or R 2.7 beta for the 
BioConductor 2.2 builds on Windows, I have hit a snag because the BioC 
build system has long path names (e.g. D:\biocbld\bbs-2.2-bioc\R) and 
these path names are not resolving properly by MiKTeX 2.7 during 
vignette construction. Take, for example, the attached vignette from 
Biobase, Bioconductor.Rnw. I have built R from source at

E:\paboyoun\bbs-2.2-bioc\R

and the session information for this R is

=== BEGIN R BLOCK == > sessionInfo()
R version 2.7.0 beta (2008-04-09 r45179)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
=== END R BLOCK ==
Now when I run Sweave on Bioconductor.Rnw using the command

=== BEGIN OS BLOCK ==E:\paboyoun>bbs-2.2-bioc\R\bin\R CMD Sweave
Bioconductor.Rnw
Writing to file Bioconductor.tex
Processing code chunks ...
 1 : term tex

You can now run LaTeX on 'Bioconductor.tex'
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: Bioconductor.Rnw
Url:
https://stat.ethz.ch/pipermail/r-devel/attachments/20080409/5d318f8f/attachment.pl

Something funky happened to my e-mail. I was trying to paste information 
related to MiKTeX and R into my message and it appears to have corrupted 
the text somehow. Anyway, the message I was trying to get across is that 
the tex file contains the path

\usepackage{E:/paboyoun/BBS-2~1.2-B/R/share/texmf/Sweave}

and MiKTeX 2.7 doesn't know how to resolve it. (The Bioconductor.tex 
file is (hopefully) attached to this e-mail.)


=== BEGIN OS BLOCK ==
E:\paboyoun>pdflatex --version
MiKTeX-pdfTeX 2.7.2987 (1.40.7) (MiKTeX 2.7)
Copyright (C) 1982 D. E. Knuth, (C) 1996-2006 Han The Thanh
TeX is a trademark of the American Mathematical Society.

E:\paboyoun>pdflatex Bioconductor.tex
This is pdfTeX, Version 3.141592-1.40.7 (MiKTeX 2.7)
entering extended mode
(Bioconductor.tex
LaTeX2e <2005/12/01>
Babel <v3.8h> and hyphenation patterns for english, dumylang, 
nohyphenation, ge
rman, ngerman, french, loaded.
("C:\Program Files\MiKTeX 2.7\tex\latex\base\article.cls"
Document Class: article 2005/09/16 v1.4f Standard LaTeX document class
("C:\Program Files\MiKTeX 2.7\tex\latex\base\size12.clo"))
("C:\Program Files\MiKTeX 2.7\tex\latex\psnfss\times.sty")
("C:\Program Files\MiKTeX 2.7\tex\latex\hyperref\hyperref.sty"
("C:\Program Files\MiKTeX 2.7\tex\latex\graphics\keyval.sty")
("C:\Program Files\MiKTeX 2.7\tex\latex\oberdiek\hycolor.sty")
("C:\Program Files\MiKTeX 2.7\tex\latex\hyperref\pd1enc.def")
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\etexcmds.sty"
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\infwarerr.sty"))
("C:\Program Files\MiKTeX 2.7\tex\latex\00miktex\hyperref.cfg")
("C:\Program Files\MiKTeX 2.7\tex\latex\oberdiek\kvoptions.sty")
Implicit mode ON; LaTeX internals redefined
("C:\Program Files\MiKTeX 2.7\tex\latex\ltxmisc\url.sty")
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\bitset.sty"
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\intcalc.sty")
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\bigintcalc.sty"
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\pdftexcmds.sty")))
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\kvsetkeys.sty")
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\atbegshi.sty"
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\ifpdf.sty")))
*hyperref using default driver hpdftex*
("C:\Program Files\MiKTeX 2.7\tex\latex\hyperref\hpdftex.def")
! Missing \endcsname inserted.
<to be read again>
                   \protect
l.28 \begin
           {document}
?